6V92

RSC-NCP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 20.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



Literature

Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement.

Patel, A.B.Moore, C.M.Greber, B.J.Luo, J.Zukin, S.A.Ranish, J.Nogales, E.

(2019) Elife 8

  • DOI: 10.7554/eLife.54449
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Eukaryotic DNA is packaged into nucleosome arrays, which are repositioned by chromatin remodeling complexes to control DNA accessibility. The Saccharomyces cerevisiae RSC ( R emodeling the S tructure of C hromatin) com ...

    Eukaryotic DNA is packaged into nucleosome arrays, which are repositioned by chromatin remodeling complexes to control DNA accessibility. The Saccharomyces cerevisiae RSC ( R emodeling the S tructure of C hromatin) complex, a member of the SWI/SNF chromatin remodeler family, plays critical roles in genome maintenance, transcription, and DNA repair. Here, we report cryo-electron microscopy (cryo-EM) and crosslinking mass spectrometry (CLMS) studies of yeast RSC complex and show that RSC is composed of a rigid tripartite core and two flexible lobes. The core structure is scaffolded by an asymmetric Rsc8 dimer and built with the evolutionarily conserved subunits Sfh1, Rsc6, Rsc9 and Sth1. The flexible ATPase lobe, composed of helicase subunit Sth1, Arp7, Arp9 and Rtt102, is anchored to this core by the N-terminus of Sth1. Our cryo-EM analysis of RSC bound to a nucleosome core particle shows that in addition to the expected nucleosome-Sth1 interactions, RSC engages histones and nucleosomal DNA through one arm of the core structure, composed of the Rsc8 SWIRM domains, Sfh1 and Npl6. Our findings provide structural insights into the conserved assembly process for all members of the SWI/SNF family of remodelers, and illustrate how RSC selects, engages, and remodels nucleosomes.


    Organizational Affiliation

    Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 7A477Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ARP7SWP61YPR034WYP9367.14
Find proteins for Q12406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear protein STH1/NPS1R1359Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: STH1NPS1YIL126W
EC: 3.6.4.12
Find proteins for P32597 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Actin-like protein ARP9B467Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ARP9SWP59YMR033WYM9973.07
Find proteins for Q05123 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Regulator of Ty1 transposition protein 102P157Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RTT102YGR275WG9378
Find proteins for P53330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
High temperature lethal protein 1C78Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HTL1DRT1YCR020W-B
Find proteins for Q9URQ5 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Chromatin structure-remodeling complex protein RSC14D180Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LDB7RSC14YBL006CYBL0322
Find proteins for P38210 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Chromatin structure-remodeling complex subunit RSC7E435Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NPL6RSC7YMR091CYM9582.16C
Find proteins for P32832 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Chromatin structure-remodeling complex subunit RSC2F889Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RSC2YLR357WL9638.1
Find proteins for Q06488 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Chromatin structure-remodeling complex protein RSC3G885Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RSC3YDR303CD9740.13
Find proteins for Q06639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Chromatin structure-remodeling complex subunit RSC4H625Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RSC4YKR008WYK107
Find proteins for Q02206 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Chromatin structure-remodeling complex protein RSC8I, J, K, L557Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RSC8SWH3YFR037C
Find proteins for P43609 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Chromatin structure-remodeling complex protein RSC6M483Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RSC6YCR052WYCR52W
Find proteins for P25632 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Chromatin structure-remodeling complex subunit RSC9N581Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RSC9YML127WYM4987.08
Find proteins for Q03124 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Chromatin structure-remodeling complex protein RSC58O502Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RSC58YLR033W
Find proteins for Q07979 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Chromatin structure-remodeling complex subunit SFH1Q426Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SFH1YLR321CL8543.4
Find proteins for Q06168 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Chromatin structure-remodeling complex protein RSC30S883Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RSC30YHR056C
Find proteins for P38781 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Unknown Protein3, 419Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Unknown Protein514Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Uuknown Protein615Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Unknown Protein749Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Histone H3.1a, e136Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P68431 (Homo sapiens)
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NIH Common Fund Data Resources
PHAROS  P68431
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Histone H4b, f103Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P62805 (Homo sapiens)
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Go to UniProtKB:  P62805
NIH Common Fund Data Resources
PHAROS  P62805
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1-B/Ec, g130Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ABH2AFMHIST1H2AEH2AFAH2AC4H2AC8
Find proteins for P04908 (Homo sapiens)
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Go to UniProtKB:  P04908
NIH Common Fund Data Resources
PHAROS  P04908
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Histone H2B type 1-Kd, h126Homo sapiensMutation(s): 0 
Gene Names: H2BC12H2BFTHIRIP1HIST1H2BK
Find proteins for O60814 (Homo sapiens)
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Go to UniProtKB:  O60814
NIH Common Fund Data Resources
PHAROS  O60814
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Unknown Protein228Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 22
MoleculeChainsLengthOrganism
DNA (146-MER)i, j146synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
I
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 20.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM63072
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35-GM127018

Revision History 

  • Version 1.0: 2020-01-15
    Type: Initial release